Novel druggable regions in set domain proteins, and methods of using the same
AssigneeEmory University
InventorsXiaodong Cheng, Xing Zhang
Life of this patent
Estimating the term…
Abstract
The present invention relates to novel druggable regions discovered in histone H3 lysine methyltransferase DIM-5, which is a SET domain protein. The present invention further relates to methods of using the druggable regions to screen potential candidate therapeutics for diseases in which the activity of SET domain proteins are implicated, for example, anti-cancer/anti-proliferative agents or anti-fungal agents.
Claims73
A method of modulating the activity of a SET domain protein comprising modulating the activity of a druggable region of said protein.
A method for identifying a candidate therapeutic for a disease caused by an organism having a SET domain protein, comprising assaying the ability of a test compound to modulate the activity of at least one druggable region of said SET protein, wherein the ability to modulate indicates a candidate therapeutic.
A method for identifying a candidate therapeutic for a disease caused by a cell or organism having a SET domain protein, comprising contacting said SET domain protein with a test compound, wherein the ability of said compound to bind to said protein indicates a candidate therapeutic.
A method for identifying a candidate therapeutic for a disease caused by a cell or organism having a SET domain protein, comprising contacting said SET domain protein with a test compound, wherein a decrease in the viability of said cell or organism indicates a candidate therapeutic.
A method for designing a candidate modulator for screening for modulators of a polypeptide, the method comprising:
- (a) providing the three dimensional structure of a druggable region of a polypeptide comprising (1) an amino acid sequence comprising a histone lysine methyltransferase protein having SEQ ID NO:
- 1;
- or (2) an amino acid sequence having at least about 85% identity with SEQ ID NO:
- 1;
- and
- (b) designing a candidate modulator based on the three dimensional structure of the druggable region of the polypeptide.
A method for designing a modulator of the activity of a histone lysine methyltransferase protein, comprising:
- (a) providing a three-dimensional structure comprising:
- (1) an amino acid sequence comprising a histone lysine methyltransferase protein having SEQ ID NO:
- 1;
- or (2) an amino acid sequence having at least about 85% identity with SEQ ID NO:
- 1;
- or (3) an amino acid sequence comprising at least one druggable region of SEQ ID NO:
- 1;
- or (4) an amino acid sequence comprising a sequence having at least about 85% identity with at least one druggable region of SEQ ID NO:
- 1;
- and having at least one biological activity of histone lysine methyltransferase protein;
- and
- (b) identifying a potential modulator by reference to the three-dimensional structure.
A method for identifying a potential modulator of a histone lysine methyltransferase polypeptide from a database, the method comprising:
- (a) providing the three-dimensional coordinates for a plurality of the amino acids of a polypeptide comprising:
- (1) an amino acid sequence comprising a histone lysine methyltransferase protein having SEQ ID NO:
- 1;
- or (2) an amino acid sequence having at least about 85% identity with SEQ ID NO:
- 1;
- or (3) an amino acid sequence comprising at least one druggable region of SEQ ID NO:
- 1;
- or (4) an amino acid sequence comprising a sequence having at least about 85% identity with at least one druggable region of SEQ ID NO:
- 1;
- and having at least one biological activity of histone lysine methyltransferase protein;
- (b) identifying a druggable region of the polypeptide;
- and
- (c) selecting from a database at least one potential modulator comprising three dimensional coordinates which indicate that the modulator may bind or interfere with the druggable region.
A computer-assisted method for identifying an modulator of the activity of a histone lysine methyltransferase polypeptide, comprising:
- (a) supplying a computer modeling application with a set of structure coordinates as listed in PDB accession number 1ML9 or FIG. 6 for the atoms of the amino acid residues from any of the above-described druggable regions of histone lysine methyltransferase polypeptide so as to define part or all of a molecule or complex;
- (b) supplying the computer modeling application with a set of structure coordinates of a chemical entity;
- and
- (c) determining whether the chemical entity is expected to bind to or interfere with the molecule or complex.
A method for preparing a potential modulator of a druggable region contained in a polypeptide, the method comprising:
- (a) using the atomic coordinates for the backbone atoms of at least about six amino acid residues from a polypeptide of SEQ ID NO:1 with a ± a root mean square deviation from the backbone atoms of the amino acid residues of not more than 5.0 Å, to generate one or more three-dimensional structures of a molecule comprising a druggable region from the polypeptide;
- (b) employing one or more of the three dimensional structures of the molecule to design or select a potential modulator of the druggable region;
- and
- (c) synthesizing or obtaining the modulator.
A computer-assisted method for identifying an inhibitor of the activity of a histone lysine methyltransferase polypeptide, comprising:
- (a) supplying a computer modeling application with a set of structure coordinates as listed in FIG. 6 or in PDB 1ML9 for the atoms of the amino acid residues from any of the above-described druggable regions of histone lysine methyltransferase polypeptide so as to define part or all of a molecule or complex;
- (b) supplying the computer modeling application with a set of structure coordinates of a chemical entity;
- and
- (c) determining whether the chemical entity is expected to bind to or interfere with the molecule or complex.
A computer-assisted method for designing an inhibitor of histone lysine methyltransferase activity comprising:
- (a) supplying a computer modeling application with a set of structure coordinates having a root mean square deviation of less than about 1.5 Å from the structure coordinates as listed in FIG. 6 or in PDB accession number 1ML9 for the atoms of the amino acid residues from any of the above-described druggable regions of histone lysine methyltransferase so as to define part or all of a molecule or complex;
- (b) supplying the computer modeling application with a set of structure coordinates for a chemical entity;
- (c) evaluating the potential binding interactions between the chemical entity and the molecule or complex;
- (d) structurally modifying the chemical entity to yield a set of structure coordinates for a modified chemical entity;
- and
- (e) determining whether the modified chemical entity is an inhibitor expected to bind to or interfere with the molecule or complex, wherein binding to or interfering with the molecule or molecular complex is indicative of potential inhibition of histone lysine methyltransferase activity.
A computer-assisted method for designing an inhibitor of histone lysine methyltransferase activity de novo comprising:
- (a) supplying a computer modeling application with a set of three-dimensional coordinates derived from the structure coordinates as listed in FIG. 6 or in PDB accession number 1ML9 for the atoms of the amino acid residues from any of the above-described druggable regions of histone lysine methyltransferase so as to define part or all of a molecule or complex;
- (b) computationally building a chemical entity represented by a set of structure coordinates;
- and
- (c) determining whether the chemical entity is an inhibitor expected to bind to or interfere with the molecule or complex, wherein binding to or interfering with the molecule or complex is indicative of potential inhibition of bistone lysine methyltransferase activity.
A method for identifying a druggable region of a histone lysine methyltransferase protein, the method comprising:
- (a) obtaining crystals of a polypeptide comprising (1) an amino acid sequence comprising a histone lysine methyltransferase protein having SEQ ID NO:
- 1;
- or (2) an amino acid sequence having at least about 85% identity with SEQ ID NO:
- 1;
- and having at least one biological activity of histone lysine methyltransferase protein, such that the three dimensional structure of the crystallized polypeptide may be determined to a resolution of 3.5 Å or better;
- (b) determining the three dimensional structure of the crystallized polypeptide using X-ray diffraction;
- and
- (c) identifying a druggable region of the crystallized polypeptide based on the three-dimensional structure of the crystallized polypeptide.
Crystalline histone lysine methyltransferase comprising a crystal having a P212121 space group.
A crystalline histone lysine methyltransferase complex.
A crystallized polypeptide comprising (1) an amino acid sequence comprising a histone lysine methyltransferase protein having SEQ ID NO:
- 1;
- or (2) an amino acid sequence having at least about 85% identity with SEQ ID NO:
- 1;
- or (3) an amino acid sequence comprising at least one druggable region of SEQ ID NO:
- 1;
- or (4) an amino acid sequence comprising a sequence having at least about 85% identity with at least one druggable region of SEQ ID NO:
- 1;
- and having at least one biological activity of a histone lysine methyl transferase protein;
- wherein the crystal has a P212121 space group.
A crystallized polypeptide comprising a structure of a polypeptide that is defined by a portion of the atomic coordinates in FIG. 6 or in PDB accession number 1ML9.
A method for determining the crystal structure of a homolog of a polypeptide, the method comprising:
- (a) providing the three dimensional structure of a first crystallized polypeptide comprising (1) an amino acid sequence comprising a histone lysine methyltransferase protein having SEQ ID NO:
- 1;
- or (2) an amino acid sequence having at least about 85% identity with SEQ ID NO:
- 1;
- or (3) an amino acid sequence comprising at least one druggable region of SEQ ID NO:
- 1;
- or (4) an amino acid sequence comprising a sequence having at least about 85% identity with at least one druggable region of SEQ ID NO:
- 1;
- and having at least one biological activity of histone lysine methyltransferase protein;
- (b) obtaining crystals of a second polypeptide comprising an amino acid sequence that is at least 50% identical to the amino acid sequence comprising SEQ ID NO:
- 1 and having at least one biological activity of histone lysine methyl transferase protein, such that the three dimensional structure of the second crystallized polypeptide may be determined to a resolution of 3.5 Å or better;
- and
- (c) determining the three dimensional structure of the second crystallized polypeptide by x-ray crystallography based on the atomic coordinates of the three dimensional structure provided in step (a).
A method for obtaining structural information about a molecule or a molecular complex of unknown structure comprising:
- (a) crystallizing the molecule or molecular complex;
- (b) generating an x-ray diffraction pattern from the crystallized molecule or molecular complex;
- (c) applying at least a portion of the structure coordinates of FIG. 6 or in PDB accession number 1ML9 to the x-ray diffraction pattern to generate a three-dimensional electron density map of at least a portion of the molecule or molecular complex whose structure is unknown.
A method for making a crystallized complex comprising a polypeptide and a candidate modulator, the method comprising:
- (a) crystallizing a polypeptide comprising (1) an amino acid sequence comprising a histone lysine methyltransferase protein having SEQ ID NO:
- 1;
- or (2) an amino acid sequence having at least about 85% identity with SEQ ID NO:
- 1;
- or (3) an amino acid sequence comprising at least one druggable region of SEQ ID NO:
- 1;
- or (4) an amino acid sequence comprising a sequence having at least about 85% identity with at least one druggable region of SEQ ID NO:
- 1;
- and having at least one biological activity of histone lysine methyltransferase protein;
- such that crystals of the crystallized polypeptide will diffract x-rays to a resolution of 5 Å or better;
- and
- (b) soaking the crystals in a solution comprising a potential modulator.
A method for incorporating a potential modulator in a crystal of a polypeptide, comprising placing a crystal of histone lysine methyl transferase protein having a space group P212121 in a solution comprising the potential modulator.
Dependencies are inferred from the claim text.